Organizational heterogeneity of vertebrate genomes

Svetlana Frenkel, Valery Kirzhner, Abraham Korol

Research output: Contribution to journalArticlepeer-review

Abstract

Genomes of higher eukaryotes are mosaics of segments with various structural, functional, and evolutionary properties. The availability of whole-genome sequences allows the investigation of their structure as "texts" using different statistical and computational methods. One such method, referred to as Compositional Spectra (CS) analysis, is based on scoring the occurrences of fixed-length oligonucleotides (k-mers) in the target DNA sequence. CS analysis allows generating species- or region-specific characteristics of the genome, regardless of their length and the presence of coding DNA. In this study, we consider the heterogeneity of vertebrate genomes as a joint effect of regional variation in sequence organization superimposed on the differences in nucleotide composition. We estimated compositional and organizational heterogeneity of genome and chromosome sequences separately and found that both heterogeneity types vary widely among genomes as well as among chromosomes in all investigated taxonomic groups. The high correspondence of heterogeneity scores obtained on three genome fractions, coding, repetitive, and the remaining part of the noncoding DNA (the genome dark matter - GDM) allows the assumption that CS-heterogeneity may have functional relevance to genome regulation. Of special interest for such interpretation is the fact that natural GDM sequences display the highest deviation from the corresponding reshuffled sequences.

Original languageEnglish
Article numbere32076
JournalPLoS ONE
Volume7
Issue number2
DOIs
StatePublished - 27 Feb 2012

Bibliographical note

Funding Information:
We thank the anonymous reviewers for their helpful comments and suggestions, Dr. Zeev Frenkel for useful discussions and Alexander Frenkel for help in improving the scripts. This work was supported by the Israeli Ministry of Absorption (S.F. and V.K.). S.F. was also supported by a fellowship for excellence in Converging Technologies Program of The Council for Higher Education.

ASJC Scopus subject areas

  • General

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